Energy Efficient Multimedia Communications in IEEE 802.11 Networks

During the last decade wireless mobile communications have progressively become part of the people’s daily lives, leading users to expect to be “alwaysbest-connected” to the Internet, regardless of their location or time of day. This is indeed motivated by the fact that wireless access networks are increasingly ubiquitous, through different types of service providers, together with an outburst of thoroughly portable devices, namely laptops, tablets, mobile phones, among others. The “anytime and anywhere” connectivity criterion raises new challenges regarding the devices’ battery lifetime management, as energy becomes the most noteworthy restriction of the end-users’ satisfaction. This wireless access context has also stimulated the development of novel multimedia applications with high network demands, although lacking in energy-aware design. Therefore, the relationship between energy consumption and the quality of the multimedia applications perceived by end-users should be carefully investigated. This dissertation addresses energy-efficient multimedia communications in the IEEE 802.11 standard, which is the most widely used wireless access technology. It advances the literature by proposing a unique empirical assessment methodology and new power-saving algorithms, always bearing in mind the end-users’ feedback and evaluating quality perception. The new EViTEQ framework proposed in this thesis, for measuring video transmission quality and energy consumption simultaneously, in an integrated way, reveals the importance of having an empirical and high-accuracy methodology to assess the trade-off between quality and energy consumption, raised by the new end-users’ requirements. Extensive evaluations conducted with the EViTEQ framework revealed its flexibility and capability to accurately report both video transmission quality and energy consumption, as well as to be employed in rigorous investigations of network interface energy consumption patterns, regardless of the wireless access technology. Following the need to enhance the trade-off between energy consumption and application quality, this thesis proposes the Optimized Power save Algorithm for continuous Media Applications (OPAMA). By using the end-users’ feedback to establish a proper trade-off between energy consumption and application performance, OPAMA aims at enhancing the energy efficiency of end-users’ devices accessing the network through IEEE 802.11. OPAMA performance has been thoroughly analyzed within different scenarios and application types, including a simulation study and a real deployment in an Android testbed. When compared with the most popular standard power-saving mechanisms defined in the IEEE 802.11 standard, the obtained results revealed OPAMA’s capability to enhance energy efficiency, while keeping end-users’ Quality of Experience within the defined bounds. Furthermore, OPAMA was optimized to enable superior energy savings in multiple station environments, resulting in a new proposal called Enhanced Power Saving Mechanism for Multiple station Environments (OPAMA-EPS4ME). The results of this thesis highlight the relevance of having a highly accurate methodology to assess energy consumption and application quality when aiming to optimize the trade-off between energy and quality. Additionally, the obtained results based both on simulation and testbed evaluations, show clear benefits from employing userdriven power-saving techniques, such as OPAMA, instead of IEEE 802.11 standard power-saving approaches.

POPULATION CODING IN LAMINAR CORTICAL CIRCUITS

One of the fundamental questions in neuroscience is to understand how encoding of sensory inputs is distributed across neuronal networks in cerebral cortex to influence sensory processing and behavioral performance. The fact that the structure of neuronal networks is organized according to cortical layers raises the possibility that sensory information could be processed differently in distinct layers. The goal of my thesis research is to understand how laminar circuits encode information in their population activity, how the properties of the population code adapt to changes in visual input, and how population coding influences behavioral performance. To this end, we performed a series of novel experiments to investigate how sensory information in the primary visual cortex (V1) emerges across laminar cortical circuits. First, it is commonly known that the amount of information encoded by cortical circuits depends critically on whether or not nearby neurons exhibit correlations. We examined correlated variability in V1 circuits from a laminar-specific perspective and observed that cells in the input layer, which have only local projections, encode incoming stimuli optimally by exhibiting low correlated variability. In contrast, output layers, which send projections to other cortical and subcortical areas, encode information suboptimally by exhibiting large correlations. These results argue that neuronal populations in different cortical layers play different roles in network computations. Secondly, a fundamental feature of cortical neurons is their ability to adapt to changes in incoming stimuli. Understanding how adaptation emerges across cortical layers to influence information processing is vital for understanding efficient sensory coding. We examined the effects of adaptation, on the time-scale of a visual fixation, on network synchronization across laminar circuits. Specific to the superficial layers, we observed an increase in gamma-band (30-80 Hz) synchronization after adaptation that was correlated with an improvement in neuronal orientation discrimination performance. Thus, synchronization enhances sensory coding to optimize network processing across laminar circuits. Finally, we tested the hypothesis that individual neurons and local populations synchronize their activity in real-time to communicate information about incoming stimuli, and that the degree of synchronization influences behavioral performance. These analyses assessed for the first time the relationship between changes in laminar cortical networks involved in stimulus processing and behavioral performance.

Systems Biology Approaches to Probe Gene Regulation in Bacteria

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb). First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses and survive within resting macrophages. As a result, the method unveiled transcriptional regulators and associated regulons utilized by Mtb to establish a successful infection of macrophages throughout the first 14 days of infection. Additionally, this network-based analysis identified the production of Fe-S proteins coupled to lipid metabolism through the alkane hydroxylase complex as a possible strategy employed by Mtb to survive in the host. Second, I developed a network inference method to infer the small non-coding RNA (sRNA) regulatory network in Mtb. The method identifies sRNA-mRNA interactions by integrating a priori knowledge of possible binding sites with structure-driven identification of binding sites. The reconstructed network was useful to predict functional roles for the multitude of sRNAs recently discovered in the pathogen, being that several sRNAs were postulated to be involved in virulence-related processes. Finally, I applied a combined experimental and computational approach to study post-transcriptional repression mediated by small non-coding RNAs in bacteria. Specifically, a probabilistic ranking methodology termed rank-conciliation was developed to infer sRNA-mRNA interactions based on multiple types of data. The method was shown to improve target prediction in Escherichia coli, and therefore is useful to prioritize candidate targets for experimental validation.

Fibulin-2 stabilizes tumor extracellular matrix and drives malignant progression of lung adenocarcinoma

The ECM of epithelial carcinomas undergoes structural remodeling during periods of uncontrolled growth, creating regional heterogeneity and torsional stress. How tumors maintain ECM integrity in the face of dynamic biophysical forces is still largely unclear. This study addresses these deficiencies using mouse models of human lung adenocarcinoma. Spontaneous lung tumors were marked by disorganized basement membranes, dense collagen networks, and increased tissue stiffness. Metastasis-prone lung adenocarcinoma cells secreted fibulin-2 (Fbln2), a matrix glycoprotein involved in ECM supra-molecular assembly. Fibulin-2 depletion in tumor cells decreased the intra-tumoral abundance of matrix metalloproteinases and reduced collagen cross-linking and tumor compressive properties resulting in inhibited tumor growth and metastasis. Fbln2 deposition within intra-tumoral fibrotic bands was a predictor of poor clinical outcome in patients. Collectively, these findings support a feed-forward model in which tumor cells secrete matrix-stabilizing factors required for the assembly of ECM that preferentially favors malignant progression. To our knowledge, this is the first evidence that tumor cells directly regulate the integrity of their surrounding matrix through the secretion of matrix-stabilizing factors such as fibulin-2. These findings open a new avenue of research into matrix assembly molecules as potential therapeutic targets in cancer patients.

REGULATION OF ALTERNATIVE CARBON METABOLISM IN CANDIDA ALBICANS

Candida albicans is the most important fungal pathogen of humans. Transcript profiling studies show that upon phagocytosis by macrophages, C. albicans undergoes a massive metabolic reorganization activating genes involved in alternative carbon metabolism, including the glyoxylate cycle, β-oxidation and gluconeogenesis. Mutations in key enzymes such as ICL1 (glyoxylate cycle) and FOX2 (fatty acid β-oxidation) revealed that alternative carbon metabolic pathways are required for full virulence in C. albicans. These studies indicate C. albicans uses non-preferred carbon sources allowing its adaptation to microenvironments were nutrients are scarce. It has become apparent that the regulatory networks required for regulation of alternative carbon metabolism in C. albicans are considerably different from the Saccharomyces cerevisiae paradigm and appear more analogous to the Aspergillus nidulans systems. Well-characterized transcription factors in S. cerevisiae have no apparent phenotype or are missing in C. albicans. CTF1 was found to be a single functional homolog of the A. nidulans FarA/FarB proteins, which are transcription factors required for fatty acid utilization. Both FOX2 and ICL1 were found to be part of a large CTF1 regulon. To increase our understanding of how CTF1 regulates its target genes, including whether regulation is direct or indirect, the FOX2 and ICL1 promoter regions were analyzed using a combination of bioinformatics and promoter deletion analysis. To begin characterizing the FOX2 and ICL1 promoters, 5’ rapid amplification of cDNA ends (5’RACE) was used to identify two transcriptional initiation sites in FOX2 and one in ICL1. GFP reporter assays show FOX2 and ICL1 are rapidly expressed in the presence of alternative carbon sources. Both FOX2 and ICL1 harbor the CCTCGG sequence known to be bound by the Far proteins, hence rendering the motif as a putative CTF1 DNA binding element. In this study, the CCTCGG sequence was found to be essential for FOX2 regulation. However, this motif does not appear to be equally important for the regulation of ICL1. This study supports the notion that although C. albicans has diverged from the paradigms of model fungi, C. albicans has made specific adaptations to its transcription-based regulatory network that may contribute to its metabolic flexibility.

Pathway Semantics: An Algebraic Data Driven Algorithm to Generate Hypotheses about Molecular Patterns Underlying Disease Progression

The overarching goal of the Pathway Semantics Algorithm (PSA) is to improve the in silico identification of clinically useful hypotheses about molecular patterns in disease progression. By framing biomedical questions within a variety of matrix representations, PSA has the flexibility to analyze combined quantitative and qualitative data over a wide range of stratifications. The resulting hypothetical answers can then move to in vitro and in vivo verification, research assay optimization, clinical validation, and commercialization. Herein PSA is shown to generate novel hypotheses about the significant biological pathways in two disease domains: shock / trauma and hemophilia A, and validated experimentally in the latter. The PSA matrix algebra approach identified differential molecular patterns in biological networks over time and outcome that would not be easily found through direct assays, literature or database searches. In this dissertation, Chapter 1 provides a broad overview of the background and motivation for the study, followed by Chapter 2 with a literature review of relevant computational methods. Chapters 3 and 4 describe PSA for node and edge analysis respectively, and apply the method to disease progression in shock / trauma. Chapter 5 demonstrates the application of PSA to hemophilia A and the validation with experimental results. The work is summarized in Chapter 6, followed by extensive references and an Appendix with additional material.

Construcción de repositorios institucionales open source con Software Greenstone

Se aborda la construcción de repositorios institucionales open source con Software Greenstone. Se realiza un recorrido teórico y otro modélico desarrollando en él una aplicación práctica. El primer recorrido, que constituye el marco teórico, comprende una descripción, de: la filosofía open access (acceso abierto) y open source (código abierto) para la creación de repositorios institucionales. También abarca en líneas generales las temáticas relacionadas al protocolo OAI, el marco legal en lo que hace a la propiedad intelectual, las licencias y una aproximación a los metadatos. En el mismo recorrido se abordan aspectos teóricos de los repositorios institucionales: acepciones, beneficios, tipos, componentes intervinientes, herramientas open source para la creación de repositorios, descripción de las herramientas y finalmente, la descripción ampliada del Software Greenstone; elegido para el desarrollo modélico del repositorio institucional colocado en un demostrativo digital. El segundo recorrido, correspondiente al desarrollo modélico, incluye por un lado el modelo en sí del repositorio con el Software Greenstone; detallándose aquí uno a uno los componentes que lo conforman. Es el insumo teórico-práctico para el diseño -paso a paso- del repositorio institucional. Por otro lado, se incluye el resultado de la modelización, es decir el repositorio creado, el cual es exportado en entorno web a un soporte digital para su visibilización. El diseño del repositorio, paso a paso, constituye el núcleo sustantivo de aportes de este trabajo de tesina

Construcción de repositorios institucionales open source con Software Greenstone

Se aborda la construcción de repositorios institucionales open source con Software Greenstone. Se realiza un recorrido teórico y otro modélico desarrollando en él una aplicación práctica. El primer recorrido, que constituye el marco teórico, comprende una descripción, de: la filosofía open access (acceso abierto) y open source (código abierto) para la creación de repositorios institucionales. También abarca en líneas generales las temáticas relacionadas al protocolo OAI, el marco legal en lo que hace a la propiedad intelectual, las licencias y una aproximación a los metadatos. En el mismo recorrido se abordan aspectos teóricos de los repositorios institucionales: acepciones, beneficios, tipos, componentes intervinientes, herramientas open source para la creación de repositorios, descripción de las herramientas y finalmente, la descripción ampliada del Software Greenstone; elegido para el desarrollo modélico del repositorio institucional colocado en un demostrativo digital. El segundo recorrido, correspondiente al desarrollo modélico, incluye por un lado el modelo en sí del repositorio con el Software Greenstone; detallándose aquí uno a uno los componentes que lo conforman. Es el insumo teórico-práctico para el diseño -paso a paso- del repositorio institucional. Por otro lado, se incluye el resultado de la modelización, es decir el repositorio creado, el cual es exportado en entorno web a un soporte digital para su visibilización. El diseño del repositorio, paso a paso, constituye el núcleo sustantivo de aportes de este trabajo de tesina

Aiming at improving access to research output through the institutional repository

The paper is to introduce the institutional repository (IR) as a powerful tool to support the researchers of the institution to archive and disseminate their research findings freely to the scholarly community on the Internet. The IR can improve the access to an institution’s research output enormously. The operations of an IR also require various interactions with researchers, which enables the library to gain a solid understanding of research needs and expectations. Through such interaction, the relationship and mutual trust between researchers and the library are strengthened. The experiences of the Institute of Developing Economies (IDE) library can be useful to other special libraries.

Quantum key distribution based on selective post-processing in passive optical networks

One of the main obstacles to the widespread adoption of quantum cryptography has been the difficulty of integration into standard optical networks, largely due to the tremendous difference in power of classical signals compared with the single quantum used for quantum key distribution. This makes the technology expensive and hard to deploy. In this letter, we show an easy and straightforward integration method of quantum cryptography into optical access networks. In particular, we analyze how a quantum key distribution system can be seamlessly integrated in a standard access network based on the passive optical and time division multiplexing paradigms. The novelty of this proposal is based on the selective post-processing that allows for the distillation of secret keys avoiding the noise produced by other network users. Importantly, the proposal does not require the modification of the quantum or classical hardware specifications neither the use of any synchronization mechanism between the network and quantum cryptography devices.

Adaptive cross-device videoconferencing solution for wireless networks based on QoS monitoring

The increase in CPU power and screen quality of todays smartphones as well as the availability of high bandwidth wireless networks has enabled high quality mobile videoconfer- encing never seen before. However, adapting to the variety of devices and network conditions that come as a result is still not a trivial issue. In this paper, we present a multiple participant videoconferencing service that adapts to different kind of devices and access networks while providing an stable communication. By combining network quality detection and the use of a multipoint control unit for video mixing and transcoding, desktop, tablet and mobile clients can participate seamlessly. We also describe the cost in terms of bandwidth and CPU usage of this approach in a variety of scenarios.

Entanglement Distribution in Quantum Metropolitan Optical Networks

The ability to generate entangled photon-pairs over a broad wavelength range opens the door to the simultaneous distribution of entanglement to multiple users of a network using a single source and wavelength-division multiplexing technologies. Here we show the design of a metropolitan optical network made of tree-type access networks where entangled photon-pairs are distributed to any pair of users, independently of their location. The resulting network improves the reach, number of users and capabilities of existing proposals. Moreover, it is made up of typical commercial components and uses the existing infrastructure, which allows for moderate deployment costs. Finally, we develop a channel plan and a network design that allow direct optical communications, quantum and classical, between any pair of users. Therefore, multiple quantum information technologies can make use of this network.

Entanglement distribution in optical networks

The ability to generate entangled photon pairs over a broad wavelength range opens the door to the simultaneous distribution of entanglement to multiple users in a network by using centralized sources and flexible wavelength-division multiplexing schemes. Here, we show the design of a metropolitan optical network consisting of tree-type access networks, whereby entangled photon pairs are distributed to any pair of users, independent of their location. The network is constructed employing commercial off-the-shelf components and uses the existing infrastructure, which allows for moderate deployment costs. We further develop a channel plan and a network-architecture design to provide a direct optical path between any pair of users; thus, allowing classical and one-way quantum communication, as well as entanglement distribution. This allows the simultaneous operation of multiple quantum information technologies. Finally, we present a more flexible backbone architecture that pushes away the load limitations of the original network design by extending its reach, number of users and capabilities.

Entanglement generation and routing in optical networks

New telecom wavelength sources of polarization entangled photon pairs allow the distribution of entanglement through metro-access networks using standard equipment. This is essential to ease the deployment of future applications that can profit from quantum entanglement, such as quantum cryptography.

Integration of quantum key distribution in metropolitan area networks

The deployment of Quantum Key Distribution forces the development of QKD-links to be operated in current and next-generation photonic metro-access networks. These highly heterogeneous architectures determine the conditions QKD-links need to be optimized for.